[gmx-users] Re: crystal waters

[Marc Lensink]

On Thursday 24 June 2004 12:06, Marc Bruning wrote:
> hello,
>
> i have tried different ways to keep track of crystal waters in a
> gromacs simulation. but i always loose them because they are mixed
> with the solvent added to the protein. is there a specific way to
> add crystal waters, so they are treated seperately from the rest of
> the solvent?

make a group HOH for your crystal waters, and SOL for the solvent you
add with genbox. if you keep the crystal waters in the original
pdb-file, i think that pdb2gmx does this automatically, or at least
some previous version of gmx did this.  you should just make sure that
the groups are not merged at a later stage in your system preparation
(genion or genbox). oh, and you might have to copy spc.itp to hoh.itp
and change the molecule name therein. then #include both files.

marc